Chris wrote:
> Of course, I cannot get my own pages to work
> with Mozilla, but that is another story.
So, what kinds of problems are you having?
Do your pages work with Safari and on Win32 browsers? If so, then the
problem is probably this lack-of-LiveConnect issue.
Miguel

In January 2004 Chris wrote:
> If a user "command clicks" to activate the contexual menu and then
> changes his mind and wishes to dismiss the menu, the user must click
> inside the JmolApplet window. If the user clicks outside the JmolApplet
> window, the contextual menu will not be deactivated.
I recently spent some time looking into this.
It turns out that it is beyond my control. The popup menu code is part of
the local Java implementation.
When the popup menu appears Jmol gets a mouse event saying that the mouse
has left the applet window ... because it is now on top of the popup menu
window. No more mouse events go to Jmol.
Miguel

> I am somewhat confused about what LiveConnect does for the JmolApplet,
> which is not a big surprise. Is LiveConnect the technology that must be
> supported for JmolApplet buttons to work?
In general, the answer is "Yes".
LiveConnect is what enables communcation between JavaScript (within an
HTML page) and Java (within an applet)
> Like the buttons on this page,
>
> http://jmol.sourceforge.net/demo/alphahelix/
But not with these buttons :-) I built in special support for a special
type of button (that uses an applet) primarily because LiveConnect did not
exist on MacOS X.
> or am I way off? The reason I ask is that the above referenced page
> works with Mozilla 1.6.
As I said, these pages were built using a different technique just so that
they *would* work on OSX.
Miguel

Judith wrote:
> The double dash does not work either. When I use the double dash as
> you suggest, I get the error message I was getting using the -script in
> 10pre7 instead of the unrecognized file format message:
This works on both Linux and on Win32 ... not that this helps you very
much :-(
I don't have access to an OSX machine.
Egon, do you think we should consider using anotehr command-line option
parser?
Miguel

I am somewhat confused about what LiveConnect does for the JmolApplet,
which is not a big surprise. Is LiveConnect the technology that must be
supported for JmolApplet buttons to work? Like the buttons on this
page,
http://jmol.sourceforge.net/demo/alphahelix/
or am I way off? The reason I ask is that the above referenced page
works with Mozilla 1.6. Of course, I cannot get my own pages to work
with Mozilla, but that is another story.
Chris
On Mar 30, 2004, at 6:39 AM, Miguel wrote:
>> Perhaps Miguel was referring to LiveConnect support, not Javascript
>> support, when he was talking about the MacOS X browsers. Right now,
>> the
>> only MacOS X browsers that I know of that support LiveConnect are
>> Safari
>> 1.2 (OS 10.3 only), Opera 7.50 beta, and Netscape 7.02.
>
> With very limited testing on a slow Machine (G3 333 Mhz) I have not
> found
> Netscape 7.02 to be reliable with the JmolApplet.
>> There continue to
>> be many users who use up to OS 10.2.8 -- partly because in its wisdom,
>> Apple has decided to charge $130 to upgrade to Panther. I don't know
>> whether Jaguar can handle Java 1.4.
>>
>> For now, I don't think it's wise to require Panther, Safari 1.2, and
>> Java
>> 1.4.
>
> Uhh ... just a reminder that we are talking about *at least* 6 months
> from
> now.
>
>
> Miguel
>
>
>
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Miguel sent [5.32p gmt 2004 March 30 Tuesday] :
>>>There isn't anything in this statement which refers to LiveConnect
>>>on Mac OSX.
>>>
>>but nothing that explicitly excludes OSX, either. so I am left
>>wondering where the statement applies. Linux only? everything
>>except OSX?
>
>But they have never had OSX support ... have they?
>
no, but the statement is from the "new features' section of their doc.
perhaps it was a case of wishful thinking on my part. ;-)
>>>That is a bug ... and you should file it with the Mozilla team.
>>>
>>a bug in the report, or a bug in actually choosing the JVM? the
>>first would be merely annoying; the second would be more important.
>
>As a developer, I would say that it is a bug for them to choose 1.3
>instead of 1.4 when both are installed on the machine.
>
so they are actually using 1.3, not just reporting it incorrectly. yes,
I consider this a bug, too.
thanks for clarifying,
:tim
--=20
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/&gt;
usa:north carolina:wake forest

>>There isn't anything in this statement which refers to LiveConnect
>>on Mac OSX.
>>
> but nothing that explicitly excludes OSX, either. so I am left
> wondering where the statement applies. Linux only? everything except
> OSX?
But they have never had OSX support ... have they?
>>That is a bug ... and you should file it with the Mozilla team.
>>
> a bug in the report, or a bug in actually choosing the JVM? the first
> would be merely annoying; the second would be more important.
As a developer, I would say that it is a bug for them to choose 1.3
instead of 1.4 when both are installed on the machine.
Miguel

Miguel sent [5.00p gmt 2004 March 30 Tuesday] :
>>>>Mozilla 1.7 beta advertises this:
>>>>
>>>>" Liveconnect now works when a Java applet's codebase is in a
>>>>different domain "
>
>There isn't anything in this statement which refers to LiveConnect
>on Mac OSX.
>
but nothing that explicitly excludes OSX, either. so I am left
wondering where the statement applies. Linux only? everything except
OSX?
>However, the statement has me puzzled ... I thought that it was
>impossible to have the codebase in a different domain because it was
>a security violation.
>
>I will post a message to the Mozilla formus.
>
ok.
>>>><http://www.mozilla.org/releases/mozilla1.7b/README.html&gt;
>>well, not good news for Mozilla 1.7b on OSX:
>
>I suggest that you post a separate message inquiring about Mozilla +
>LiveConnect + OSX.
>
ok I will.
>
>>M1.7b appears to use Java 1.3 with Jmol (10pre6), according to the
>>Console output, and not Java 1.4.
>
>That is a bug ... and you should file it with the Mozilla team.
>
a bug in the report, or a bug in actually choosing the JVM? the first
would be merely annoying; the second would be more important.
regards,
:tim
--=20
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/&gt;
usa:north carolina:wake forest

>>>Mozilla 1.7 beta advertises this:
>>>
>>>" Liveconnect now works when a Java applet's codebase is in a
>>>different domain "
There isn't anything in this statement which refers to LiveConnect on Mac
OSX.
However, the statement has me puzzled ... I thought that it was impossible
to have the codebase in a different domain because it was a security
violation.
I will post a message to the Mozilla formus.
>>><http://www.mozilla.org/releases/mozilla1.7b/README.html&gt;
> well, not good news for Mozilla 1.7b on OSX:
I suggest that you post a separate message inquiring about Mozilla +
LiveConnect + OSX.
> M1.7b appears to use Java 1.3 with Jmol (10pre6), according to the
> Console output, and not Java 1.4.
That is a bug ... and you should file it with the Mozilla team.
Miguel

timothy driscoll sent [6.04a gmt 2004 March 30 Tuesday] :
>timothy driscoll sent [5.54a gmt 2004 March 30 Tuesday] :
>
>>Robert B. Grossman sent [5.36a gmt 2004 March 30 Tuesday] :
>>
>>>For now, I don't think it's wise to require Panther, Safari 1.2,
>>>and Java 1=3D3D3D ..4. If Mozilla/Netscape comes out with a newer
>>>browser that works on Jag=3D3D3D uar, supports LiveConnect, *and*
>>>uses Java 1.4, I'll reconsider my positi=3D3D3D on.
>>>
>>Mozilla 1.7 beta advertises this:
>>
>>" Liveconnect now works when a Java applet's codebase is in a
>>different domain "
>>
>><http://www.mozilla.org/releases/mozilla1.7b/README.html&gt;
>>
>>
well, not good news for Mozilla 1.7b on OSX:
I am not able to get LiveConnect to work, at least within the scope of
Jmol 10pre6. =20
>well I just found this about Mozilla 1.7b, too:
>
>
>Java J2SE releases previous to 1.3.0_01 will not work with Mozilla.
>Problems have been reported with JRE 1.3.1. For best results JRE
>1.4.1 is recommended. Mozilla has been tested with all 1.3.0_*
>versions of the JRE, and JRE 1.3.1, and beta versions of JDK 1.4.
>
><http://www.mozilla.org/releases/mozilla1.7b/known-issues.html#java&gt;
>
M1.7b appears to use Java 1.3 with Jmol (10pre6), according to the
Console output, and not Java 1.4.
in addition, Mozilla 1.7b is *still* not compliant with javascript
standard DOM references. grr.
so I guess the real meaning of the Mozilla 1.7b readme document escapes
me. it sure sounds like LC and Java 1.4 should be usable. oh well.
back to Safari ;-)
:tim
--=20
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/&gt;
usa:north carolina:wake forest

> Perhaps Miguel was referring to LiveConnect support, not Javascript
> support, when he was talking about the MacOS X browsers. Right now, the
> only MacOS X browsers that I know of that support LiveConnect are Safari
> 1.2 (OS 10.3 only), Opera 7.50 beta, and Netscape 7.02.
With very limited testing on a slow Machine (G3 333 Mhz) I have not found
Netscape 7.02 to be reliable with the JmolApplet.
> There continue to
> be many users who use up to OS 10.2.8 -- partly because in its wisdom,
> Apple has decided to charge $130 to upgrade to Panther. I don't know
> whether Jaguar can handle Java 1.4.
>
> For now, I don't think it's wise to require Panther, Safari 1.2, and Java
> 1.4.
Uhh ... just a reminder that we are talking about *at least* 6 months from
now.
Miguel

> Many thanks for including support for CIF files, Miguel!
>
> I certainly did not expect it so quickly!
>
> So, how does Jmol handle a CIF file with more than one structure in it?
It doesn't :-)
It will either stop after the first one or will build one model that has
everything dumped together ... don't know :-)
Miguel

Phil wrote:
>>Not exactly true...
>>
>>http://news.com.com/2100-1012-5087678.html
>>'MICROSOFT EXTENDS SUPPORT FOR ITS JAVA MACHINE
>>
>>(Last modified: October 7, 2003, 3:50 AM PDT)
>>Microsoft will continue to support its Java virtual machine through
>> September 2004, a nine-month extension that will make it easier for
>> customers to find substitutes for the software...'
Here is my understanding of the situation ...
'Support' from Microsoft means security bug fixes ... nothing more. That
is, if you already have the JVM installed then you can get security fixes.
However, I don't think that one can use Windows Update to install the old
JVM on XP systems. This has been the case for some time.
Jan wrote:
> I argue against cutting off MSJVM until September 2004, than MS will
> regard the MSJVM as insecure and it will not longer work without
> lowering the IE browsers security policy, so the user has to take action
> in any case.
This is an interesting point. And in a business setting I think that one
could argue (somewhat politically) that 'security risk' was a valid reason
for not supporting the IE JVM.
However, I don't think that has any impact on legacy systems for students
and universities.
There is nothing magical about the Sept 2004 date.
>>And even after that cutoff date, _all_ the installed JVMs are going to
>> continue to operate, and that's a lot of machines! Now this is not an
>> issue for the developers and their/our machines...it's an issue from
>> at-home students
* Actually, those at-home students with dial-up lines will get some great
benefits from the newer JVM. The Java Plugin has a large separate cache
for applets. Therefore, they will only have to download the JmolApplet
one time from a given site. As long as the JmolApplet does not change on
the web site then they won't need to download it again.
* During the download process they will see a progress bar, giving them
visual feedback of how long it will take. -- On the MSFT JVM they see
nothing.
* With the newer JVM I can structure things so that they are in multiple
.jar files. The first .jar file can have a 'directory' which says which
jar files contain which classes. Therefore, only the jar files that are
needed will get downloaded. -- On the old JVMs all jar files get
downloaded.
* The JmolApplet is going to get larger. We are currently at 400K and I
suspect that we will be at 750K - 1Mb by the time we finish adding
support for file formats and features.
With the size we have today we are looking at a 1.5 to 2 minute download
over a dialup line. That delay is going to grow to 3 or 4. During this
download they get NO feedback. And next week when they go back to the same
site, they have to wait again.
With the Sun JVM they download once, the download what they need, and they
get visual feedback of how long it is going to take.
>> instructions to download other software or to reach into the bowels of IE
>> preferences and toggle between the Sun and Microsoft Java machines.
No toggling needs to be done. They install the Sun plugin and it works.
>>It may not be 'fair' to other OS and browser choices with VMs, but
>> pragmatically Jmol should not abandon use on Microsoft JVM if there is
>> not a technical reason to do so.
I think that there are technical and practical reasons.
I assure you that we share the same goal ... to reach as many users as
possible. And 90% are on Win32. I just don't think that they are going to
wait for 2 to 4 minutes each time they go a site that has the JmolApplet.
Q: Do you think that there is value in a JmolAppletLite that could run on
old JVMs and eliminated a lot of functionality?
Q: If so, what functionality would you be willing to jettison?
>>(OTOH, I can see abandoning NS 4.x, etc., because they are dinosaurs
>> _and_ virtually none of the traffic to my site uses them anyway, even if
>> they are chime-capable--can others who keep website statistics verify a
>> need to try to keep them?)
Actually, it turns out that there is very little to be gained by dropping.
The debugging has already been done to support NS4 & MacOS 9. So if we
maintain support for the MSFT JVM then we may as well leave in the code
for them too.
Let's keep talking.
Miguel

Robert B. Grossman sent [5.36a gmt 2004 March 30 Tuesday] :
>Perhaps Miguel was referring to LiveConnect support, not Javascript
>support=3D , when he was talking about the MacOS X browsers. Right
>now, the only Ma=3D cOS X browsers that I know of that support
>LiveConnect are Safari 1.2 (OS=3D 10.3 only), Opera 7.50 beta, and
>Netscape 7.02. There continue to be ma=3D ny users who use up to OS
>10.2.8 -- partly because in its wisdom, Apple h=3D as decided to
>charge $130 to upgrade to Panther. I don't know whether Ja=3D guar
>can handle Java 1.4. =3D20
>
as much as I complained about paying this price, and I did complain
quite loudly, the .1 increase is very misleading. the differences
between 10.2 and 10.3 are substantial enough to make it well worth the
price. but that's quite OT, I realize. :-)
>For now, I don't think it's wise to require Panther, Safari 1.2, and
>Java 1=3D ..4. If Mozilla/Netscape comes out with a newer browser
>that works on Jag=3D uar, supports LiveConnect, *and* uses Java 1.4,
>I'll reconsider my positi=3D on.
>
Mozilla 1.7 beta advertises this:
"
Liveconnect now works when a Java applet's codebase is in a different
domain
"
<http://www.mozilla.org/releases/mozilla1.7b/README.html&gt;
I will check out what exactly *that* means by downloading the beta in a
few hours (in a rush right now...). unless you get to it first, Bob.
:-)
regards,
:tim
--=20
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/&gt;
usa:north carolina:wake forest

Forgive me if I jump into this conversation with some irrelevant informatio=
n, but...
I agree that there are still many MacOS 9 users out there, and an option fo=
r them is worthwhile. Chime has to be registered and downloaded before y=
ou can use it. The Jmol applet, on the other hand, can be delivered dire=
ctly to a novice user. =20
Perhaps Miguel was referring to LiveConnect support, not Javascript support=
, when he was talking about the MacOS X browsers. Right now, the only Ma=
cOS X browsers that I know of that support LiveConnect are Safari 1.2 (OS=
10.3 only), Opera 7.50 beta, and Netscape 7.02. There continue to be ma=
ny users who use up to OS 10.2.8 -- partly because in its wisdom, Apple h=
as decided to charge $130 to upgrade to Panther. I don't know whether Ja=
guar can handle Java 1.4. =20
For now, I don't think it's wise to require Panther, Safari 1.2, and Java 1=
.4. If Mozilla/Netscape comes out with a newer browser that works on Jag=
uar, supports LiveConnect, *and* uses Java 1.4, I'll reconsider my positi=
on.
-- Bob
-------------------------------------
Note the new email address suffix!
Prof. Robert B. Grossman
Department of Chemistry
University of Kentucky
Chemistry-Physics Building
Lexington, KY 40506-0055
Tel.: (859) 257-1285
Fax: (859) 323-1069
Cell: (859) 312-1285
mailto:rbgros1@...
http://www.chem.uky.edu/research/grossman/
Check out "The Art of Writing Reasonable Organic Reaction Mechanisms" at:
http://www.chem.uky.edu/research/grossman/textbook.html =01

Many thanks for including support for CIF files, Miguel!
I certainly did not expect it so quickly!
So, how does Jmol handle a CIF file with more than one structure in it?
-------------------------------------
Note the new email address suffix!
Prof. Robert B. Grossman
Department of Chemistry
University of Kentucky
Chemistry-Physics Building
Lexington, KY 40506-0055
Tel.: (859) 257-1285
Fax: (859) 323-1069
Cell: (859) 312-1285
mailto:rbgros1@...
http://www.chem.uky.edu/research/grossman/
Check out "The Art of Writing Reasonable Organic Reaction Mechanisms" at:
http://www.chem.uky.edu/research/grossman/textbook.html =01

PHILLIP W BARAK schrieb:
>----- Original Message -----
>From: Miguel <miguel@...>
>
>
>
>>I have a series of questions regarding compatibility and minimum JVM
>>requirements for the JmolApplet. I am interested in your feedback.
>>
>>Proposal: drop support for old JVMs
>>-----------------------------------
>>
>>I have put a tremendous amount of energy into dealing with the quirky
>>behavior of some of these older JVMs. Therefore, it is with some
>>sadness/anxiety/concern that I am making the following proposal:
>>
>> I propose that Jmol v10 *require* Java 1.4
>> This will remove some of the 'baggage' associated with the old
>> web browser JVMs and will allow us to take advantage of new
>> features that are found in the current releases of Java.
>>
>> <clipped>
>>
>>Therefore, anyone running Internet Explorer on XP must install the Sun
>>Java Plug-in in order to be able to run any web applet.
>>
>>
>
>
>Not exactly true...
>
>http://news.com.com/2100-1012-5087678.html
>'MICROSOFT EXTENDS SUPPORT FOR ITS JAVA MACHINE
>
>(Last modified: October 7, 2003, 3:50 AM PDT)
>Microsoft will continue to support its Java virtual machine through September 2004, a nine-month extension that will make it easier for customers to find substitutes for the software...'
>
>And even after that cutoff date, _all_ the installed JVMs are going to continue to operate, and that's a lot of machines! Now this is not an issue for the developers and their/our machines...it's an issue from at-home students and other users who log onto our Jmol sites and then get instructions to download other software or to reach into the bowels of IE preferences and toggle between the Sun and Microsoft Java machines.
>
>Simply based on my site statistics, the _great_ majority of visitors' identifiable OSs and browsers are of the MS variety--I didn't ask for it that way, but there's no point arguing with them. And I'd rather not disappoint them by sending them off site without showing them some of the goods, especially if the MS JVM is reasonably fast and technically compatible with Jmol!
>
>(I recall the havoc created when IE on XP shipped for a while without JVM...I started getting multiple reports that a few pages with a Java applet 'didn't work')
>
>It may not be 'fair' to other OS and browser choices with VMs, but pragmatically Jmol should not abandon use on Microsoft JVM if there is not a technical reason to do so.
>
>(OTOH, I can see abandoning NS 4.x, etc., because they are dinosaurs _and_ virtually none of the traffic to my site uses them anyway, even if they are chime-capable--can others who keep website statistics verify a need to try to keep them?)
>
>
>
Last month statistics of single count IP from outside the institute
74% Windows
10% Linux
9% Mac
2% IRIX
1% SUN
rest: Free-BSD, HP-UX, OS/2 and mobile devices: Nocia, SonyEricson
using:
57% MSIE
26% Gecko
11% Netscape4.x
1% Opera
1% Konqueror
rest: Mozilla2/3/5, Lynx, libwww-FM, Jakarta
I argue against cutting off MSJVM until September 2004, than MS will
regard the MSJVM as insecure and it will not longer work without
lowering the IE browsers security policy, so the user has to take action
in any case.
Downloading 15 MB SUNJVM is not easy for a student with dial-up internet
connection, which are about 40% (more than 10 subnet IPs per month
identified, not uni- not edu) at our site.
Regards, Jan
>None of the above goes to the longer term picture, which is definitely to follow Java back to Sun entirely, across all browsers and platforms. But let us not lead the pack unless there is a clear advantage to having others trailing behind us.
>
>--Phil 'please, not the bleeding edge, again' Barak
>
>